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GeneBe

3-180912712-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_005087.4(FXR1):c.27C>T(p.Arg9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00574 in 1,613,834 control chromosomes in the GnomAD database, including 435 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.030 ( 230 hom., cov: 32)
Exomes 𝑓: 0.0032 ( 205 hom. )

Consequence

FXR1
NM_005087.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0850
Variant links:
Genes affected
FXR1 (HGNC:4023): (FMR1 autosomal homolog 1) The protein encoded by this gene is an RNA binding protein that interacts with the functionally-similar proteins FMR1 and FXR2. These proteins shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-180912712-C-T is Benign according to our data. Variant chr3-180912712-C-T is described in ClinVar as [Benign]. Clinvar id is 791961.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.085 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FXR1NM_005087.4 linkuse as main transcriptc.27C>T p.Arg9= synonymous_variant 1/17 ENST00000357559.9
FXR1NM_001013438.3 linkuse as main transcriptc.27C>T p.Arg9= synonymous_variant 1/16
FXR1NM_001013439.3 linkuse as main transcriptc.-573C>T 5_prime_UTR_variant 1/18
FXR1NM_001363882.1 linkuse as main transcriptc.-573C>T 5_prime_UTR_variant 1/17

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FXR1ENST00000357559.9 linkuse as main transcriptc.27C>T p.Arg9= synonymous_variant 1/171 NM_005087.4 P51114-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0297
AC:
4511
AN:
151914
Hom.:
228
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.104
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00917
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000603
Gnomad OTH
AF:
0.0192
GnomAD3 exomes
AF:
0.00798
AC:
2006
AN:
251426
Hom.:
78
AF XY:
0.00575
AC XY:
782
AN XY:
135892
show subpopulations
Gnomad AFR exome
AF:
0.104
Gnomad AMR exome
AF:
0.00581
Gnomad ASJ exome
AF:
0.00149
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000416
Gnomad NFE exome
AF:
0.000528
Gnomad OTH exome
AF:
0.00570
GnomAD4 exome
AF:
0.00324
AC:
4742
AN:
1461804
Hom.:
205
Cov.:
34
AF XY:
0.00282
AC XY:
2049
AN XY:
727220
show subpopulations
Gnomad4 AFR exome
AF:
0.108
Gnomad4 AMR exome
AF:
0.00637
Gnomad4 ASJ exome
AF:
0.00134
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000185
Gnomad4 FIN exome
AF:
0.000300
Gnomad4 NFE exome
AF:
0.000308
Gnomad4 OTH exome
AF:
0.00644
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0297
AC:
4516
AN:
152030
Hom.:
230
Cov.:
32
AF XY:
0.0287
AC XY:
2134
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.104
Gnomad4 AMR
AF:
0.00916
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000603
Gnomad4 OTH
AF:
0.0190
Alfa
AF:
0.00669
Hom.:
40
Bravo
AF:
0.0340
Asia WGS
AF:
0.00375
AC:
13
AN:
3478
EpiCase
AF:
0.000654
EpiControl
AF:
0.000533

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeAug 15, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.26
Cadd
Benign
16
Dann
Benign
0.96
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1805578; hg19: chr3-180630500; COSMIC: COSV59764939; COSMIC: COSV59764939; API